Repository to collect and share bed files for each bait set. This repository does not contain any bait information. There is also plan to add annotations for each bed file.
| Source code | https://github.com/Clinical-Genomics/target_capture_bed |
|---|---|
| Build status |  |
| Version |  |
| Repository size |  |
| Development model | Github Flow |
| Maintainers | Hassan Foroughi, Anna Lyander, Keyvan Elhami |
List of current panels¶
| id | short name | file name | designer |
|---|---|---|---|
| CG2.1 | lymphomatic_2.1 | lymphomatic_2.1_hg19_design.bed | Christian Brieghel |
| CG3.1 | gi_cfdna_3.1 | gicfdna_3.1_hg19_design.bed | Emma Tham |
| CG4.1 | gmck_solid_4.1 | gmcksolid_4.1_hg19_design.bed | Johan Lindberg |
| CG5.1 | gms_myeloid_5.1 | gmsmyeloid_5.1_hg19_design.bed | Christina Orsmark Pietras |
| CG5.2 | gms_myeloid_5.2 | gmsmyeloid_5.2_hg19_design.bed | Christina Orsmark Pietras |
| CG6.1 | lymphoma_6.1 | lymphoma_6.1_hg19_design.bed | Valtteri Wirta |
| CG7.1 | gms_lymphoid_7.1 | gmslymphoid_7.1_hg19_design.bed | Christina Orsmark Pietras |
| CG8.1 | exome_8.1 | twistexome_8.1_hg19_design.bed | Twist Bioscience |
| CG9.1 | exome_refseq_9.1 | twistexomerefseq_9.1_hg19_design.bed | Twist Bioscience |
| CG10.1 | exome_comp_10.1 | twistexomecomprehensive_10.1_hg19_design.bed | Twist Bioscience |
| CG11.1 | agilent_sureselect_cre_11.1 | agilentsureselectcre_11.1_hg19_design.bed | Agilent |
| CG12.1 | agilent_sureselect_v5_12.1 | agilentsureselectv5_12.1_hg19_design.bed | Agilent |
| CG13.1 | agilent_sureselect_v1_13.1 | agilentsureselectv1_13.1_hg19_design.bed | Agilent |
lymphomatic_2.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 26548 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep |
gi_cfdna_3.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 76261 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep |
gmck_solid_4.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 1705152 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep | HD832 (OncoSpan FFPE, Horizon Discovery) |
gms_myeloid_5.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 712494 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep | HD829 (Myeloid DNA Reference Standard, Horizon Discovery) |
gms_myeloid_5.2¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 728436 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v2 |
| Control sample in library prep | HD829 (Myeloid DNA Reference Standard, Horizon Discovery) |
lymphoma_6.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 159268 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep |
gms_lymphoid_7.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 1957492 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep | HD829 (Myeloid DNA Reference Standard, Horizon Discovery) |
exome_8.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 33053262 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep | NA24143 (Coriell Institute) |
exome_refseq_9.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 36339084 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep | NA24143 (Coriell Institute) |
exome_comp_10.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 36363631 bp |
| Genome version | hg19 |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep | NA24143 (Coriell Institute) |
agilent_sureselect_cre_11.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 54098923 bp |
| Genome version | |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep |
agilent_sureselect_v5_12.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 50390601 bp |
| Genome version | |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep |
agilent_sureselect_v1_13.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 51542852 bp |
| Genome version | |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep |
agilent_sureselect_focused_exome_v1_14.1¶
| Feature type | Count |
|---|---|
| Genes | 000 |
| Unique Transcripts | 000 |
| Transcripts with all exons covered | 000 |
| Transcripts with at least one exon covered | 000 |
| Design Padding | 000bp |
| Panel size | 17846036 bp |
| Genome version | |
| COSMIC SNPs | 000 |
| Non-genic regions | 000bp |
| Number of independendant segments | 000 |
| Version | v1 |
| Control sample in library prep |
Filename convention¶
{project_name}_{project_number.version}_{genome_version}_{application/purpose}.{file_extension}
example1: GMCKsolid_4.1_hg19_design.bed
example2: GMCKsolid_4.1_hg38_design.bed
example3: TwistExome_8.1_hg19_design.bed
example4: TwistExomeRefSeq_9.1_hg19_design.bed
project_name¶
Name will reflect company or project name for the bed. Examples: GMCKsolid or TwistExomeRefSeq
project_number¶
Integer starting from 1 and new projects will get a new number.
version¶
Any change to regions or features in the original design file.
genome_version¶
hg19, hg38
application/purpose¶
- target: original target file that was sent to Twist
- design: all_target_segments_covered_by_probes file received from Twist
- dropout: all_target_segments_not_covered_by_probes file received from Twist
- ucsctrack: file is suitable to upload to ucsc as track file. Same file as target but with a header suitable to upload to UCSC genome browser
file_extension¶
- bed: bed can be bed3, 4, 6, 12 columns
- bedgraph/bigwig: standard bedgraph and bigwig format from ucsc
Versioning Schema¶
This change log will document the notable changes to this project in this file and it is following Semantic Versioning. The version numbering consists of three digits: major.minor.patch:
- major: addition, updating, or removing following items from a bed file:
- Genome version
- Region size (even 1bp) (e.g. chr:Start-End)
- Target bed name (not file name). (e.g. GMCKSolid to GMCKsolid or GMCKsolidtumor)
- minor: addition, updating, or removing following items:
- External URLs
- annotations and features
- file name (i.e. not panel name)
- patch: addition, updating, or removing following items:
- README (designer, description, typo)